ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaatacttcaaaattgtgcatttctcattgtttcagatttcagaagttgaggcaacttagcactagctcatcaatgttataggctcaaggcacgt...

Basic information

species	Zea mays
transcript	GRMZM2G037200_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G037200_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g45480.2 (Oryza sativa), 5'ss of exon 3

TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacg----taatacttcaaaattgtgcattt--ctcattgtttcagatttca-gaagttgaggcaacttagcactagctcatcaatgttataggctcaaggcacgt
||||||||||||||||  ||||| |||||| | ||||| ||||||| ||| || || |||||||||||||| || || ||||| ||||||||| |    | | || | | | |||||  |||   |||    |   | | | | |  ||| | |     |    ||| ||     ||  ||| ||  |  || |   
TGTGCTGGTGTCATCAATATGGGACGTGAGATCGGGTGCATGATCAGTGAGGGGCCATGGTTATTTGTTGGGATTCCAGATGCTGTGAAGgtagggcgattagacctgagatttgtgactttgcttcagcactattggtgtaatggtgttcatgtg---tgtgtctatctgcctgat-ctattggtacttggtatag

upper sequence: GRMZM2G037200_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g45480.4 (Oryza sativa), 5'ss of exon 1

----------TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacg----taatacttcaaaattgtgcattt--ctcattgtttcagatttca-gaagttgaggcaacttagcactagctcatcaatgttataggctcaaggcacgt
          ||||||||||||||||  ||||| |||||| | ||||| ||||||| ||| || || |||||||||||||| || || ||||| ||||||||| |    | | || | | | |||||  |||   |||    |   | | | | |  ||| | |     |    ||| ||     ||  ||| ||  |  || |   
CCTGTGTTAGTGTGCTGGTGTCATCAATATGGGACGTGAGATCGGGTGCATGATCAGTGAGGGGCCATGGTTATTTGTTGGGATTCCAGATGCTGTGAAGgtagggcgattagacctgagatttgtgactttgcttcagcactattggtgtaatggtgttcatgtg---tgtgtctatctgcctgat-ctattggtacttggtatag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|149095550|gb|EE181207.2|EE181207

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|93282169|gb|EB674433.1|EB674433

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGGGAC-AACTG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGG--ACCAACTG

EST: gi|29576800|gb|CB616912.1|CB616912

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|31997696|gb|CD661719.1|CD661719

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|148948214|gb|EC893730.2|EC893730

EST:     TGATCATTGAGGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCCACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|149086361|gb|EE175902.2|EE175902

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GGTTTGGA-TATGCAAACAGCAGCGGAAATGAGCCCTACTGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagG-TTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGG

EST: gi|26559549|gb|CA831784.1|CA831784

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|22715752|gb|BU197942.1|BU197942

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|22819542|gb|BU499632.1|BU499632

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|29576814|gb|CB616926.1|CB616926

EST:     TCATTTGAAGGTCCGTGGGTTATTTGTTCGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TCA-TTGAAGGTCCGT-GGTTATTTGTT-GGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

EST: gi|149070982|gb|EE159387.2|EE159387

EST:     GATCATTGAAGGTCCGTGGTTATTTTGTTGGAATACCTGATGCAATGAAG                         GTTTGGAATATG
genomic: GATCATTGAAGGTCCGTGGTTATTT-GTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATG

EST: gi|211300821|gb|FL154798.1|FL154798

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGA
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGA

EST: gi|87157418|gb|DY402207.1|DY402207

EST:     TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAG                         GTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG
genomic: TGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 120

TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaata ... tttacttcagGTTTGGAATATGCAAACAGCAGCGGAAATGAGCCTTACTGGACCAACTGGGCAAGTCTATGCACTCGCCGTTGCCAGTGAGTTACTCTTTGCTGCAACAC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 203

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGCTGGTGTCATCACCATGGGTCGTGAGGTTGGGTGTATGATCATTGAAGGTCCGTGGTTATTTGTTGGAATACCTGATGCAGTGAAGgtacgtaatacttcaaaattgtgcatttctcattgtttcagatttcagaagttgaggcaacttagcactagctcatcaatgttataggctcaaggcacgt

- - - - - - - - - - - - - - - - - - - - - - - TTGAAG